Synthetic Biology:Tools

Via this page, we hope to maintain a collection of links to online tools that are related to Synthetic Biology

DNA Tools

• Vector NTI by Informax, Inc.
  • Free-to-academics Windows-only tool for sequence analysis and data management.
• Biopolymer calculator by Schepartz lab
  • Calculate extinction coefficients, Tm's, and base composition for your DNA or RNA; calculate amino acid composition and extinction coefficient for your protein

RNA Tools

• mFold by Michael Zuker. This is the main page with links to sites for predicting RNA and DNA folds, calculating Tm's and free energies.

Protein Tools

• Zinc Finger Tools by Barbas Lab
  • Design Zinc Finger DNA binding proteins
• ExPASy Proteomics server
  • Collection of links to many pages to calculate parameters of your favorite proteins

General Tools

• Registry of Standard Biological Parts
• Colibri E. coli genome site; get sequences, see the position of your gene in the chromosome, see the function of your gene, and other fun stuff